Genome-wide association study identifies 74 loci associated with educational attainment

Using genomic structural equation modeling to examine the genetic architecture of PTSD and life satisfaction phenotypes

Objective: Posttraumatic stress disorder (PTSD) and life satisfaction phenotypes are inversely related on a phenotypic level. Given these established relations, researchers have begun to examine possible shared genetic contributions to these outcomes, though the existing genetic literature is sparse and examines these relations via univariate methods. We sought to examine the genetic architecture of PTSD and six life satisfaction and well-being phenotypes (i.e. subjective well-being, friend satisfaction, life satisfaction, family satisfaction, work satisfaction, and financial satisfaction) using a multivariate approach.Method: We used Genomic Structural Equation Modeling (gSEM) to analyze summary-level genetic data from large-scale GWAS of the European Ancestry.Results: Findings show that a two, correlated factors model fit the data best, in which PTSD and life satisfaction phenotypes load on separate but correlated factors.Conclusions: Findings suggest that, using multivariate methods, a latent factor capturing many different positive phenotypes is genetically related to PTSD. This finding confirms and extends prior phenotypic work demonstrating that PTSD and positive phenotypes are inversely related.

Educational attainment, body mass index, and smoking as mediators in kidney disease risk: a two-step Mendelian randomization study

BACKGROUND

Educational attainment (EA) has been linked to various health outcomes, including kidney disease (KD). However, the underlying mechanisms remain unclear. This study aims to assess the causal relationship between EA and KD and quantify the mediation effects of modifiable risk factors using a Mendelian randomization (MR) approach.

METHODS

We performed a two-sample MR analysis utilizing summary statistics from large-scale European genome-wide association studies (GWAS). EA (NGWAS = 766,345) was used as the exposure, and KD (Ncase/Ncontrol= 5,951/212,871) was the outcome. A two-step MR method was applied to identify and quantify the mediation effects of 24 candidate risk factors.

RESULTS

Each additional 4.2 years of genetically predicted EA was associated with a 32% reduced risk of KD (odds ratio [OR] 0.68; 95% confidence interval [CI] 0.56, 0.83). Among the 24 candidate risk factors, body mass index (BMI) mediated 21.8% of this protective effect, while smoking heaviness mediated 18.7%.

CONCLUSIONS

This study provides robust evidence that EA exerts a protective effect against KD, partially mediated by BMI and smoking. These findings highlight the potential for targeted public health interventions aimed at mitigating obesity and smoking-related risks to reduce KD incidence, particularly among individuals with lower educational attainment.

Schizophrenia genetic risk and labour market outcomes in the Finnish general population: Are schizophrenia-related traits penalised or rewarded?

BACKGROUND

Schizophrenia polygenic risk scores (SCZPRS) have been linked to cognitive functioning, creativity, behavioural traits, and psychiatric conditions beyond schizophrenia. This study examines how labour market segments reward or penalise traits associated with SCZPRS in the general population.

METHODS

We merged genetic, socio-economic and health registry data with repeated cross-sectional survey data from six Finnish cohorts (1992 to 2017), representing individuals aged 25-64 across Finnish regions (N = 20,121). Various regression models were employed to study labour market outcomes.

RESULTS

Individuals in the highest SCZPRS quintile were 6.4 percentage points less likely to be employed than those in the lowest quintile (P < 0.001; 99.5 % CI: 3.9-9.0 pp). Among employed individuals in knowledge-based occupations, an inverse U-shaped relationship between SCZPRS and income emerged after 2000. Knowledge workers in both the lowest (P = 0.004) and highest (P = 0.03) SCZPRS quintiles were 4-5 percentage points less likely to be in the highest income tertile than those in the middle quintile. No significant association was found between SCZPRS and income in physical labour.

CONCLUSIONS

Beyond its overall negative association with employment, SCZPRS exhibits a non-linear relationship with income in cognitive-intensive occupations, where both low and high SCZPRS appear to be penalised. This pattern became more pronounced post-2000, coinciding with rising income inequality and technological advancements, likely reshaping labour market demands. While effect sizes are substantial, compensatory factors may mitigate these outcomes. Greater awareness of these associations and individual differences in labour market experiences could contribute to a more inclusive society.

Emergence versus Reductionism in Science Publications

Just a few years after the U.S. government's decision to fully fund the Human Genome Project (HGP) in 1990, an important harbinger of things to come was the publication of the controversial 1994 book The Bell Curve by Richard J. Herrnstein and Charles Murray. The authors' most controversial claim was that human intelligence was at least 60 percent genetic. At that time, the national advisory group to the HGP, the Ethical Legal and Social Implications committee (ELSI) requested that the American Journal of Human Genetics critique and respond to the authors' claim. The editorial board of the journal refused on the grounds that "this book was about behavioral genetics" while the HGP was about human molecular genetics. Members of ELSI committee argued vigorously that this distinction between different forums and platforms used to explain human genetic variation would soon collapse and merge. However, it was only a matter of time before behavioral geneticists would claim the legitimacy of being under the mantle of molecular genetics. In this address, I show just how prescient the ELSI group had been. Much of the answer lies in the reward structure for science publications that strongly favor reductionism versus emergence.

PIGEON: a statistical framework for estimating gene-environment interaction for polygenic traits

Understanding gene-environment interaction (GxE) is crucial for deciphering the genetic architecture of human complex traits. However, current statistical methods for GxE inference face challenges in both scalability and interpretability. Here we introduce PIGEON-a unified statistical framework for quantifying polygenic GxE using a variance component analytical approach. Based on this framework, we outline the main objectives in GxE studies and introduce an estimation procedure that requires only summary statistics data as input. We demonstrate the effectiveness of PIGEON through theoretical and empirical analyses, including a quasi-experimental gene-by-education study of health outcomes and gene-by-sex interaction for 530 traits using UK Biobank. We also identify genetic interactors that explain the treatment effect heterogeneity in a clinical trial on smoking cessation. PIGEON suggests a path towards polygenic, summary statistics-based inference in future GxE studies.

Intelligence, brain structure, dendrites, and genes: Genetic, epigenetic and the underlying of the quadruple helix complexity

Intelligence can be referred to as the mental ability to learn, comprehend abstract concepts, and solve complex problems. Twin and adoption studies have provided insights into the influence of the familial environment and highlighted the importance of heritability in the development of cognition. Detecting the relative contribution of brain areas, neuronal structures, and connectomes has brought some understanding on how various brain areas, white/gray matter structures and neuronal connectivity process information and contribute to intelligence. Using histological, anatomical, electrophysiological, neuropsychological, neuro-imaging and molecular biology methods, several key concepts have emerged: 1) the parietofrontal-hippocampal integrations probably constitute a substrate for smart behavior, 2) neuronal activity results in structural plasticity of dendritic branches responsible for information transfer, critical for learning and memory, 3) intelligent people process information efficiently, 4) the environment triggers mnemonic epigenomic programs (via dynamic regulation of chromatin accessibility, DNA methylation, loop interruption/formation and histone modification) conferring cognitive phenotypes throughout life, and 5) single/double DNA breaks are prominent in human brain disorders associated with cognitive impairment including Alzheimer's disease and schizophrenia. Along with these observations, molecular/cellular/biological studies have identified sets of specific genes associated with higher scores on intelligence tests. Interestingly, many of these genes are associated with dendritogenesis. Because dendrite structure/function is involved in cognition, the control of dendrite genesis/maintenance may be critical for understanding the landscape of general/specific cognitive ability and new pathways for therapeutic approaches.

Enduring Mental Health in Childhood and Adolescence: Prevalence, Prediction, and Genetic Architecture

OBJECTIVE

The concept of Enduring Mental Health (EMH) describes a long-term state in which an individual does not experience mental disorders. As most people encounter mental health issues at some point, this study investigates the prevalence, predictors, and genetic architecture of EMH across childhood.

METHOD

EMH status was based on longitudinal data from 18,884 Dutch twins assessed at ages 3, 5, 7, 10, and 12 for behavioral and emotional problems. Children were grouped into three categories: EMH, some instances of mental health problems (SIMHP), and many instances of mental health problems (MIMHP). Child and parent level factors including individual polygenic scores were tested for associations with these three categories. A twin model was used to assess the contribution of genetic and environmental factors to EMH.

RESULTS

Thirty-seven percent of the sample had EMH. EMH was associated with parental education (OR(low) =0.77[0.70-0.86]; OR(middle) = 0.88[0.82-0.95]), child academic achievement (OR=1.07[1.03,1.12]), and child wellbeing (OR=1.44[1.35,1.54]), and was weakly associated with some polygenic scores. The twin model estimated that 54% of the variance in EMH was due to genetic factors.

CONCLUSION

EMH was observed in just over a third of children. Individual differences in EMH were influenced by various sociodemographic factors, mental health-related variables, and genetic predispositions, suggesting that strategies to support EMH will likely require a comprehensive, multifaceted approach.

Raising the Floor? Genetic Influences on Educational Attainment Through the Lens of the Evolving Swedish Welfare State

Interest in the role of genetics in influencing key life outcomes such as educational attainment has grown quickly. However, the question of whether genetic influences on educational attainment, on average as well as in conjunction with socioeconomic circumstances, are moderated by macro-level factors has not yet received sufficient attention. This study combines polygenic indices for educational attainment (EA PGI) with high-quality register data in a large sample of Swedish twins of European ancestry born 1920-1999. Employing both conventional between-family and within-family models, the analyses suggest that the influences of education-related genetic propensities on educational attainment have increased in Sweden during the twentieth century, a period featuring major expansions of the Swedish educational system, and decreasing economic inequality. The analyses also suggest that the degree to which socioeconomic background enhances genetic influences on education has decreased across cohorts. Genetic influences on education do not appear to have translated into increased genetic influences on income. Additionally, there is some evidence of floor and ceiling effects in the analyses of dichotomous educational outcomes.

Socio-economic status is a social construct with heritable components and genetic consequences

In civilizations, individuals are born into or sorted into different levels of socio-economic status (SES). SES clusters in families and geographically, and is robustly associated with genetic effects. Here we first review the history of scientific research on the relationship between SES and heredity. We then discuss recent findings in genomics research in light of the hypothesis that SES is a dynamic social construct that involves genetically influenced traits that help in achieving or retaining a socio-economic position, and can affect the distribution of genes associated with such traits. Social stratification results in people with differing traits being sorted into strata with different environmental exposures, which can result in evolutionary selection pressures through differences in mortality, reproduction and non-random mating. Genomics research is revealing previously concealed genetic consequences of the way society is organized, yielding insights that should be approached with caution in pursuit of a fair and functional society.

Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability

Maintenance of genome integrity is paramount to molecular programs in multicellular organisms. Throughout the lifespan, various endogenous and environmental factors pose persistent threats to the genome, which can result in DNA damage. Understanding the functional consequences of DNA damage requires investigating their preferred genomic distributions and influences on gene regulatory programs. However, such analysis is hindered by both the complex cell-type compositions within organs and the high background levels due to the stochasticity of damage formation. To address these challenges, we developed Paired-Damage-seq for joint analysis of oxidative and single-stranded DNA damage with gene expression in single cells. We applied this approach to cultured HeLa cells and the mouse brain as a proof of concept. Our results indicated the associations between damage formation and epigenetic changes. The distribution of oxidative DNA damage hotspots exhibits cell-type-specific patterns; this selective genome vulnerability, in turn, can predict cell types and dysregulated molecular programs that contribute to disease risks.

Prolonged leisure time television watching as a risk factor for chronic obstructive pulmonary disease: Insights from Mendelian randomization

Leisure sedentary behaviors are associated with an increased risk of chronic obstructive pulmonary disease (COPD), but whether this relationship is causal remains unknown. This study aimed to identify genetic determinants associated with leisure sedentary behaviors and estimate their potential causal effect on COPD risk. COPD case-control data were obtained from the Finnish biobank. Genome wide association analyses of leisure television watching, leisure computer use, and driving behavior in the UK Biobank identify 110, 82 and 6 genetic loci (P ＜ 5 × 10-8), respectively. A 2-sample Mendelian randomization (MR) analysis estimated a causal relationship between a 1.5-hour increase in television watching and a rise in COPD risk (OR = 2.725, 95% CI = 1.989-3.777, P = 7.113 × 10-10). This relationship persisted independently of age at smoking initiation, daily cigarette consumption, educational years, and body mass index in comprehensive MR analyses. However, multivariate MR analyses showed that genetically predicted leisure time spent on computers and driving did not robustly influence COPD risk. In conclusion, this MR study suggests that a genetic predisposition for prolonged time spent watching television significantly increases the risk of COPD, corroborating findings from observational studies.

Examining causal relationships between educational attainment and type 2 diabetes using genetic analysis: findings from the EPIC-InterAct study through Mendelian randomisation

INTRODUCTION

Observational studies have shown that more educated people are at lower risk of developing type 2 diabetes (T2D). However, robust study designs are needed to investigate the likelihood that such a relationship is causal. This study used genetic instruments for education to estimate the effect of education on T2D using the Mendelian randomisation (MR) approach.

METHODS

Analyses have been conducted in the European Prospective Investigation into Cancer and Nutrition (EPIC)-InterAct study (more than 20 000 individuals), a case-cohort study of T2D nested in the EPIC cohort. Education was measured as Years of Education and Relative Index of Inequality. Prentice-weighted Cox models were performed to estimate the association between education and T2D. One-sample MR analyses investigated whether genetic predisposition towards longer education was associated with risk of T2D and investigated potential mediators of the association.

RESULTS

MR estimates indicated a risk reduction of about 15% for each year of longer education on the risk of developing T2D, confirming the protective role estimated by observational models (HR 0.96, 95% CI 0.95 to 0.96). MR analyses on putative mediators showed a significant role of education on body mass index, alcohol consumption, adherence to the Mediterranean diet and smoking habits.

CONCLUSION

The results supported the hypothesis that higher education is a protective factor for the risk of developing T2D. Based on its position in the causal chain, education may be antecedent of other known risk factors for T2D including unhealthy behaviours. These findings reinforce evidence obtained through observational study designs and bridge the gap between correlation and causation.

Association Between Educational Attainment and Chronic Pain: A Mediation Mendelian Randomization Study

Background

The underlying association between educational attainment (EA) and chronic pain (CP) risk is not clear. This study aimed to investigate the causal relationship of EA with CP using Mendelian randomization (MR).

Methods

Single nucleotide polymorphisms (SNPs) for EA were selected from the Social Science Genetic Association Consortium (SSGAC). Inverse-variance weighted (IVW), weighted median, penalized weighted median, maximum likelihood (ML), and MR-Egger methods were used to estimate causal effects. Two sample MR analyses were undertaken to assess whether EA has a causal effect on CP. We also performed mediation analyses to estimate the mediation effects.

Results

A genetically predicted higher EA was associated with a decreased risk of multisite chronic pain (MCP) (odds ratio [OR] = 0.772, 95% confidence interval [CI] 0.732-0.816 per one standard deviation of longer education, P < 0.05), and the Genome-wide association studies (GWAS) data for chronic widespread pain (CWP) supported the result mentioned above. Potential mediators included body mass index (BMI) (OR = 1.176, 95% CI 1.091-1.267, P < 0.05), smoking (OR = 1.054, 95% CI 1.028-1.081, P < 0.05), and depression (OR = 1.201, 95% CI 1.147-1.258, P < 0.05) have all been proven to be causally associated with MCP. The proportions of the effects of genetically predicted EA mediated through genetically predicted BMI, smoking, and depression were 17.1%, 23.6%, and 9.2%, respectively.

Conclusion

Genetically predicted higher educational attainment reduces multisite chronic pain risk, partially mediated by body mass index (17.1%), smoking (23.6%), and depression (9.2%), highlighting education's protective role and its potential in chronic pain prevention strategies.

Associations between common genetic variants and income provide insights about the socio-economic health gradient

We conducted a genome-wide association study on income among individuals of European descent (N = 668,288) to investigate the relationship between socio-economic status and health disparities. We identified 162 genomic loci associated with a common genetic factor underlying various income measures, all with small effect sizes (the Income Factor). Our polygenic index captures 1-5% of income variance, with only one fourth due to direct genetic effects. A phenome-wide association study using this index showed reduced risks for diseases including hypertension, obesity, type 2 diabetes, depression, asthma and back pain. The Income Factor had a substantial genetic correlation (0.92, s.e. = 0.006) with educational attainment. Accounting for the genetic overlap of educational attainment with income revealed that the remaining genetic signal was linked to better mental health but reduced physical health and increased risky behaviours such as drinking and smoking. These findings highlight the complex genetic influences on income and health.

Testing the Causal Association Between Metabolic Syndrome and Periodontitis: A Two-sample Mendelian Randomisation Study

INTRODUCTION AND AIMS

Observational studies suggest an association between metabolic syndrome (MetS) and periodontitis. However, observational studies are susceptible to reverse causation and confounding factors, so the causality of this association is uncertain. Causal association between compounds of MetS and periodontitis has been well studied. Using Mendelian randomisation (MR), we aimed to comprehensively evaluate the bidirectional relationship between MetS as a whole and periodontitis and provide clinical insight.

METHODS

We used genetic instruments from the most comprehensive genome-wide association studies of European descent for MetS (n = 291,107) as well as periodontitis from both the FinnGen consortium (n = 195,395) and GeneLifestyle Interactions in Dental Endpoints (GLIDE, n = 45,563) consortium to investigate the causal relationship between MetS and periodontitis and vice versa. We used the inverse-variance weighted (IVW) method to derive the primary causal estimates and evaluated the robustness of our results with a series of sensitivity analyses.

RESULTS

MR analysis based on FinnGen consortium indicated a negative causal association of MetS on periodontitis (OR = 0.882, 95% CI = 0.791-0.983, P = .023), while MR analysis based on GLIDE consortium did not support a causal relation of MetS on periodontitis (OR = 0.986, 95% CI = 0.920-1.057, P = .697). These results were consistent after adjusting for potential confounding factors by multivariable MR analyses. Results from meta analysis did not support a causal association of MetS on periodontitis. Sensitivity analysis showed that there was no existence of pleiotropy. In the reverse direction, periodontitis showed no association with MetS.

CONCLUSIONS

Within the scope of this MR study, MetS and periodontitis are not causally related.

CLINICAL RELEVANCE

Further studies are needed to clarify the underlying mechanism between metabolic syndrome and periodontitis.

No Evidence of Interaction Between FADS2 Genotype and Breastfeeding on Cognitive or Other Traits in the UK Biobank

Breastfeeding is hypothesised to benefit child health and cognitive functioning by providing long-chain polyunsaturated fatty acids, which are essential for brain development. In 2007, Caspi et al. found evidence in two cohorts for an interaction between genetic variation in the FADS2 gene (a gene involved in fatty acid metabolism) and breastfeeding on IQ. However, subsequent studies have provided mixed evidence for the existence of an interaction. We investigated the relationship between genetic variation in the FADS2 region, breastfeeding, and their interaction in up to 335,650 individuals from the UK Biobank. We tested for the interaction over a range of cognitive functioning tests, as well as educational attainment and other traits thought to be influenced by breastfeeding, including cardiometabolic traits, number of offspring, and atopic allergy. FADS2 alleles associated with an increase in docosahexaenoic acid in blood serum (the C allele of rs174575) were associated with decreased verbal-numerical reasoning ( p = 2.28 × 10 - 5 ) and triglycerides ( p = 1.40 × 10 - 41 ), increased number of offspring ( p = 3.40 × 10 - 5 ), total cholesterol ( p = 5.28 × 10 - 36 ), HDL ( p = 1.42 × 10 - 51 ), and LDL cholesterol ( p = 1.46 × 10 - 21 ). We observed no evidence of an interaction in any of the traits, regardless of the modelling strategy on any cognitive or non-cognitive traits. We postulate that the previous positive findings are likely to be spurious, perhaps due to lack of appropriate control for latent population structure.

Neuropsychiatric polygenic scores are weak predictors of professional categories

Polygenic scores (PGS) enable the exploration of pleiotropic effects and genomic dissection of complex traits. Here, in 421,889 individuals with European ancestry from the Million Veteran Program and UK Biobank, we examine how PGS of 17 neuropsychiatric traits are related to membership in 22 broad professional categories. Overall, we find statistically significant but weak (the highest odds ratio is 1.1 per PGS standard deviation) associations between most professional categories and genetic predisposition for at least one neuropsychiatric trait. Secondary analyses in UK Biobank revealed independence of these associations from observed fluid intelligence and sex-specific effects. By leveraging aggregate population trends, we identified patterns in the public interest, such as the mediating effect of education attainment on the association of attention-deficit/hyperactivity disorder PGS with multiple professional categories. However, at the individual level, PGS explained less than 0.5% of the variance of professional membership, and almost none after we adjusted for education and socio-economic status.

Contribution of copy number variations to education, socioeconomic status and cognition from a genome-wide study of 305,401 subjects

Educational attainment (EA), socioeconomic status (SES) and cognition are phenotypically and genetically linked to health outcomes. However, the role of copy number variations (CNVs) in influencing EA/SES/cognition remains unclear. Using a large-scale (n = 305,401) genome-wide CNV-level association analysis, we discovered 33 CNV loci significantly associated with EA/SES/cognition, 20 of which were novel (deletions at 2p22.2, 2p16.2, 2p12, 3p25.3, 4p15.2, 5p15.33, 5q21.1, 8p21.3, 9p21.1, 11p14.3, 13q12.13, 17q21.31, and 20q13.33, as well as duplications at 3q12.2, 3q23, 7p22.3, 8p23.1, 8p23.2, 17q12 (105 kb), and 19q13.32). The genes identified in gene-level tests were enriched in biological pathways such as neurodegeneration, telomere maintenance and axon guidance. Phenome-wide association studies further identified novel associations of EA/SES/cognition-associated CNVs with mental and physical diseases, such as 6q27 duplication with upper respiratory disease and 17q12 (105 kb) duplication with mood disorders. Our findings provide a genome-wide CNV profile for EA/SES/cognition and bridge their connections to health. The expanded candidate CNVs database and the residing genes would be a valuable resource for future studies aimed at uncovering the biological mechanisms underlying cognitive function and related clinical phenotypes.

Genetic architectures of childhood maltreatment and causal influence of childhood maltreatment on health outcomes in adulthood

Childhood maltreatment is increasingly recognized as a pivotal risk factor for adverse health outcomes. However, comprehensive analyses of its long-term impact are scarce. This study aims to fill this gap by examining the genetic architectures of childhood maltreatment and its influence on adult health and socioeconomic outcomes. Utilizing data from the UK Biobank (N = 129,017), we conducted sex-combined and sex-stratified genome-wide association studies to identify genomic loci associated with five childhood maltreatment subtypes. We then performed genetic correlation and Mendelian randomization (MR) analyses to assess the effects of childhood maltreatment on high-burden diseases, healthcare costs, lifespan, and educational attainment. We identified several novel loci for childhood maltreatment, including one locus for sexual abuse in sex-combined analysis, one novel locus for sexual abuse in males, one locus for emotional neglect in females, and one locus for sexual abuse in females. The pairwise genetic correlations between subtypes of childhood maltreatment were moderate to high, and similar patterns of genetic correlations between childhood maltreatment subtypes were observed in males and females. Childhood maltreatment was genetically correlated with ten out of 16 high-burden diseases significantly after multiple testing correction. Moreover, MR analyses suggest childhood maltreatment may increase the risk of age-related and other hearing loss, low back pain, major depressive disorder, and migraine in adulthood, and reduce the lifespan. Our study elucidates the genetic architecture of specific childhood maltreatment subtypes and the influence of childhood maltreatment on health outcomes in adulthood, highlighting the enduring influence of childhood maltreatment on lifelong health consequences. It is important to develop prevention strategies to lower the incidence of childhood maltreatment and provide support and care for victims of childhood maltreatment for better long-term health outcomes in the population.

Associations of Education Attainment With Postpartum Depression and the Mediating Exploration: A Mendelian Randomization Study

Background: Many studies have explored the relationship between education and postpartum depression (PPD), with inconsistent results. Our study is to identify which education-related factors (education attainment, qualifications, cognitive performance) played the predominant role in PPD using Mendelian randomization (MR) analysis. Then, we explored the factors that may mediate the effect of education on PPD. Method: We performed two-sample multivariable Mendelian randomization (MVMR) to assess the independent impact of education-related factors on PPD. Based on the literature review, three mediating factors that may play a role in the path of education attainment and PPD were involved in mediation analysis, including childbearing age, neuroticism score, and average total household income before tax. Then, we used two-step MR and MVMR to estimate the indirect effect of these mediators. Results: We identified genetically predicted 1-SD (3.71 years) higher education attainment (OR: 0.632; [95% confidential interval (CI): 0.464-0.860]); qualifications (OR: 0.418; [95% CI: 0.245-0.714]); or cognitive performance (OR: 0.770; [95% CI: 0.652-0.909]) was associated with lower risk of PPD, and the causal effects of education attainment (OR: 0.407; [95% CI: 0.214-0.773]) on PPD were independent of qualifications and cognition. Childbearing age (β: -0.497; [95% CI: -0.788-0.238]; p  < 0.001) and neuroticism score (β: -0.07; [95% CI: -0.120-0.030]; p  < 0.001) were identified as mediators of the association between education attainment and PPD. Conclusions: These results suggested the predominant impact of education attainment on PPD independent of qualifications and cognition. Education level mainly affects PPD by changing the childbearing age. Trial Registration: Chinese Clinical Trial Registry identifier: ChiCTR2000033433.

Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants

Kidney dysfunction is a major cause of mortality, but its genetic architecture remains elusive. In this study, we conducted a multiancestry genome-wide association study in 2.2 million individuals and identified 1026 (97 previously unknown) independent loci. Ancestry-specific analysis indicated an attenuation of newly identified signals on common variants in European ancestry populations and the power of population diversity for further discoveries. We defined genotype effects on allele-specific gene expression and regulatory circuitries in more than 700 human kidneys and 237,000 cells. We found 1363 coding variants disrupting 782 genes, with 601 genes also targeted by regulatory variants and convergence in 161 genes. Integrating 32 types of genetic information, we present the "Kidney Disease Genetic Scorecard" for prioritizing potentially causal genes, cell types, and druggable targets for kidney disease.

Classification of schizophrenia, bipolar disorder and major depressive disorder with comorbid traits and deep learning algorithms

Many psychiatric disorders share genetic liabilities, but whether these shared liabilities can be utilized to classify and differentiate psychiatric disorders remains unclear. In this study, we use polygenic risk scores (PRSs) of 42 traits comorbid with schizophrenia (SCZ), bipolar disorder (BIP), and major depressive disorder (MDD) to evaluate their utilities. We found that combining target specific PRS with PRSs of comorbid traits can improve the classification of the target disorders. Importantly, without inclusion of PRSs from targeted disorders, we can still classify SCZ (accuracy 0.710 ± 0.008, AUC 0.789 ± 0.011), BIP (accuracy 0.782 ± 0.006, AUC 0.852 ± 0.004), and MDD (accuracy 0.753 ± 0.019, AUC 0.822 ± 0.010). Furthermore, PRSs from comorbid traits alone can effectively differentiate unaffected controls and patients with SCZ, BIP, and MDD (accuracy 0.861 ± 0.003, AUC 0.961 ± 0.041). Our results demonstrate that shared liabilities can be used effectively to improve the classification and differentiation of these disorders. The finding that PRSs from comorbid traits alone can classify and differentiate SCZ, BIP and MDD reasonably well implies that a majority of the risk variants composing target PRSs are shared with comorbid traits. Overall, our results suggest that a data-driven approach may be feasible to classify and differentiate these disorders.

A Litmus Test for Confounding in Polygenic Scores

Polygenic scores (PGSs) are being rapidly adopted for trait prediction in the clinic and beyond. PGSs are often thought of as capturing the direct genetic effect of one's genotype on their phenotype. However, because PGSs are constructed from population-level associations, they are influenced by factors other than direct genetic effects, including stratification, assortative mating, and dynastic effects ("SAD effects"). Our interpretation and application of PGSs may hinge on the relative impact of SAD effects, since they may often be environmentally or culturally mediated. We developed a method that estimates the proportion of variance in a PGS (in a given sample) that is driven by direct effects, SAD effects, and their covariance. We leverage a comparison of a PGS of interest based on a standard GWAS with a PGS based on a sibling GWAS-which is largely immune to SAD effects-to quantify the relative contribution of each type of effect to variance in the PGS of interest. Our method, Partitioning Genetic Scores Using Siblings (PGSUS, pron. "Pegasus"), breaks down variance components further by axes of genetic ancestry, allowing for a nuanced interpretation of SAD effects. In particular, PGSUS can detect stratification along major axes of ancestry as well as SAD variance that is "isotropic" with respect to axes of ancestry. Applying PGSUS, we found evidence of stratification in PGSs constructed using large meta-analyses of height and educational attainment as well as in a range of PGSs constructed using the UK Biobank. In some instances, a given PGS appears to be stratified along a major axis of ancestry in one prediction sample but not in another (for example, in comparisons of prediction in samples from different countries, or in ancient DNA vs. contemporary samples). Finally, we show that different approaches for adjustment for population structure in GWASs have distinct advantages with respect to mitigation of ancestry-axis-specific and isotropic SAD variance in PGS. Our study illustrates how family-based designs can be combined with standard population-based designs to guide the interpretation and application of genomic predictors.

Polygenic prediction of occupational status GWAS elucidates genetic and environmental interplay in intergenerational transmission, careers and health in UK Biobank

Socioeconomic status (SES) impacts health and life-course outcomes. This genome-wide association study (GWAS) of sociologically informed occupational status measures (ISEI, SIOPS, CAMSIS) using the UK Biobank (N = 273,157) identified 106 independent single-nucleotide polymorphisms of which 8 are novel to the study of SES. Genetic correlations with educational attainment (rg = 0.96-0.97) and income (rg = 0.81-0.91) point to a common genetic factor for SES. We observed a 54-57% reduction in within-family predictions compared with population-based predictions, attributed to indirect parental effects (22-27% attenuation) and assortative mating (21-27%) following our calculations. Using polygenic scores from population predictions of 5-10% (incremental R2 = 0.023-0.097 across different approaches and occupational status measures), we showed that (1) cognitive and non-cognitive traits, including scholastic and occupational motivation and aspiration, link polygenic scores to occupational status and (2) 62% of the intergenerational transmission of occupational status cannot be ascribed to genetic inheritance of common variants but other factors such as family environments. Finally, links between genetics, occupation, career trajectory and health are interrelated with parental occupational status.

The Genetics of Intelligence

BACKGROUND

Intelligence is defined as general mental capacity, which includes the abilities to reason, solve new problems, think abstractly, and learn quickly. Genetic factors explain a considerable fraction of inter-individual differences in intelligence. For many years, research on intelligence was limited to estimating the relative importance of genetic and environmental factors, without identifying any individual causal factors.

METHODS

This review of the literature is based on pertinent original publications and reviews.

RESULTS

Genome-wide association studies (GWAS) have shown that certain gene loci are associated with intelligence, as well as with educational attainment, which is known to be correlated with intelligence. As each individual gene locus accounts for only a very small part of the variance in intelligence ( < 0.02%), so-called "polygenic scores" (PGS) have been calculated in which thousands of genetic variants are summarized together. On the basis of the largest GWAS performed to date, it is estimated that 7-15% of inter-individual differences in educational attainment and 7-10% in intelligence among persons of European descent can be explained by genetic factors. These genetic effects are partly indirect. At the same time, the relative importance of genetic factors in determining complex features such as intelligence and educational attainment must always be seen against the background of individual environmental conditions. In the presence of difficult social conditions, for example, the influence of genetic factors is typically lower.

CONCLUSION

At present, the polygenic scores generated from genome-wide association studies are primarily of scientific interest, yet they are becoming increasingly informative and valid for individual prediction. There is, therefore, a need for broad social discussion about their future use.

Exome sequencing identifies genes for socioeconomic status in 350,770 individuals

Socioeconomic status (SES) is a critical factor in determining health outcomes and is influenced by genetic and environmental factors. However, our understanding of the genetic structure of SES remains incomplete. Here, we conducted a large-scale exome study of SES markers (household income, occupational status, educational attainment, and social deprivation) in 350,770 individuals. For rare coding variants, we identified 56 significant associations by gene-based collapsing tests, unveiling 7 additional SES-associated genes (NRN1, CCDC36, RHOB, EP400, NCAM1, TPTEP2-CSNK1E, and LINC02881). Exome-wide single common variant analysis revealed nine lead single-nucleotide polymorphisms (SNPs) associated with household income and 34 lead SNPs associated with EduYears, replicating previous GWAS findings. The gene-environment correlations had a substantial impact on the genetic associations with SES, as indicated by the significantly increased P values in several associations after controlling for geographic regions. Furthermore, we observed the pleiotropic effects of SES-associated genetic factors on a wide range of health outcomes, such as cognitive function, psychosocial status, and diabetes. This study highlights the contribution of coding variants to SES and their associations with health phenotypes.

A genetic exploration of the relationship between posttraumatic stress disorder and cardiovascular diseases

Experiencing a traumatic event may lead to Posttraumatic Stress Disorder (PTSD), including symptoms such as flashbacks and hyperarousal. Individuals suffering from PTSD are at increased risk of cardiovascular disease (CVD), but it is unclear why. This study assesses shared genetic liability and potential causal pathways between PTSD and CVD. We leveraged summary-level data of genome-wide association studies (PTSD: N = 1,222,882; atrial fibrillation (AF): N = 482,409; coronary artery disease (CAD): N = 1,165,690; hypertension (HT): N = 458,554; heart failure (HF): N = 977,323). First, we estimated genetic correlations and utilized genomic structural equation modeling to identify a common genetic factor for PTSD and CVD. Next, we assessed biological, behavioural, and psychosocial factors as potential mediators. Finally, we employed multivariable Mendelian randomization to examine causal pathways between PTSD and CVD, incorporating the same potential mediators. Significant genetic correlations were found between PTSD and CAD, HT, and HF (rg = 0.21-0.32, p ≤ 3.08 · 10-16), but not between PTSD and AF. Insomnia, smoking, alcohol dependence, waist-to-hip ratio, and inflammation (IL6, C-reactive protein) partly mediated these associations. Mendelian randomization indicated that PTSD causally increases CAD (IVW OR = 1.53, 95% CIs = 1.19-1.96, p = 0.001), HF (OR = 1.44, CIs = 1.08-1.92, p = 0.012), and to a lesser degree HT (OR = 1.25, CIs = 1.05-1.49, p = 0.012). While insomnia, smoking, alcohol, and inflammation were important mediators, independent causal effects also remained. In addition to shared genetic liability between PTSD and CVD, we present strong evidence for causal effects of PTSD on CVD. Crucially, we implicate specific lifestyle and biological mediators (insomnia, substance use, inflammation) which has important implications for interventions to prevent CVD in PTSD patients.

Novel Genes Associated With Working Memory Are Identified by Combining Connectome, Transcriptome, and Genome

Working memory (WM) plays a crucial role in human cognition. Previous candidate and genome-wide association studies have reported many genetic variations associated with WM. However, little research has examined genetic basis of WM by using transcriptome, even though it reflects gene function more directly than does the genome. Here we propose a new approach to exploring the genetic mechanisms of WM by integrating connectome, transcriptome, and genome data in a high-quality dataset comprising 481 Chinese healthy adults. First, relevance vector regression was used to define WM-related brain regions. Second, genes differentially expressed within these regions were identified using the Allen Human Brain Atlas (AHBA) dataset. Finally, two independent datasets were used to validate these genes' contributions to WM. With this method, we identified 24 novel genes and 20 of them were confirmed in the large-scale datasets of ABCD and UK Biobank. These novel genes were enriched in the cellular component of collagen-containing extracellular matrix and the CCL18 signaling pathway. Our method offers an effective approach to integrating multimodal gene discovery and demonstrates the superiority of expression data. This new method and the newly identified genes deserve more attention in the future.

Education, intelligence, and 20 gastrointestinal disorders: A Mendelian randomization study

Previous observational studies have suggested that higher levels of education attainment and intelligence (IQ) are associated with better health outcomes in humans. However, the causal link between education attainment and IQ and their association with health outcomes remains unclear. This study aims to investigate the distinct impacts of intelligence and educational attainment on gastrointestinal symptoms. From the genome-wide association between educational attainment and the IQ study database, results were obtained from the FinnGen summary database. We used univariate and multivariate Mendelian randomization (MR) techniques to explore the relationship between exposures and outcomes. To assess the validity of inverse-variance-weighted-based results, we used several supplementary analytical techniques and performed sensitivity analysis. Our multivariate MR study confirmed the findings from univariable analyses and showed a genetically predicted causal association between educational attainment and 8 gastrointestinal disorders, including gastroesophageal reflux disease, chronic gastritis, gastroduodenal ulcer, cirrhosis, cholelithiasis, acute pancreatitis, chronic pancreatitis, and irritable bowel syndrome. Our univariate MR study found an association between IQ and 6 gastrointestinal conditions: gastroesophageal reflux disease, cirrhosis, cholelithiasis, acute pancreatitis, pancreatic malignancy, and irritable bowel syndrome. However, the connection was much weaker in multivariate MR analysis. Our study revealed causal relationships between gastrointestinal disorders and educational attainment. Educational attainment may mediate between intelligence and the impacts on the gastrointestinal system. However, further research is required to understand the underlying pathogenic processes completely.

Charting the shared genetic architecture of Alzheimer's disease, cognition, and educational attainment, and associations with brain development

The observation that the risk of developing Alzheimer's disease is reduced in individuals with high premorbid cognitive functioning, higher educational attainment, and occupational status has led to the 'cognitive reserve' hypothesis. This hypothesis suggests that individuals with greater cognitive reserve can tolerate a more significant burden of neuropathological changes before the onset of cognitive decline. The underpinnings of cognitive reserve remain poorly understood, although a shared genetic basis between measures of cognitive reserve and Alzheimer's disease has been suggested. Using the largest samples to date and novel statistical tools, we aimed to investigate shared genetic variants between Alzheimer's disease, and measures of cognitive reserve; cognition and educational attainment to identify molecular and neurobiological foundations. We applied the causal mixture model (MiXeR) to estimate the number of trait-influencing variants shared between Alzheimer's disease, cognition, and educational attainment, and condFDR/conjFDR to identify shared loci. To provide biological insights loci were functionally characterized. Subsequently, we constructed a Structural Equation Model (SEM) to determine if the polygenic foundation of cognition has a direct impact on Alzheimer's disease risk, or if its effect is mediated through established risk factors for the disease, using a case-control sample from the UK Biobank. Univariate MiXeR analysis (after excluding chromosome 19) revealed that Alzheimer's disease was substantially less polygenic (450 trait-influencing variants) compared to cognition (11,100 trait-influencing variants), and educational attainment (12,700 trait-influencing variants). Bivariate MiXeR analysis estimated that Alzheimer's disease shared approximately 70 % of trait-influencing variants with cognition, and approximately 40 % with educational attainment, with mixed effect directions. Using condFDR analysis, we identified 18 loci jointly associated with Alzheimer's disease and cognition and 6 loci jointly associated with Alzheimer's disease and educational attainment. Genes mapped to shared loci were associated with neurodevelopment, expressed in early life, and implicated the dendritic tree and phosphatidylinositol phosphate binding mechanisms. Spatiotemporal gene expression analysis of the identified genes showed that mapped genes were highly expressed during the mid-fetal period, further suggesting early neurodevelopmental stages as critical periods for establishing cognitive reserve which affect the risk of Alzheimer's disease in old age. Furthermore, our SEM analysis showed that genetic variants influencing cognition had a direct effect on the risk of developing Alzheimer's disease, providing evidence in support of the neurodevelopmental hypothesis of the disease.

Genes, culture, and scientific racism

Quantitative studies of cultural evolution and gene-culture coevolution (henceforth "CE" and "GCC") emerged in the 1970s, in the aftermath of the "race and intelligence quotient (IQ)" and "human sociobiology" debates, as a counter to extreme hereditarian positions. These studies incorporated cultural transmission and its interaction with genetics in contributing to patterns of human variation. Neither CE nor GCC results were consistent with racist claims of ubiquitous genetic differences between socially defined races. We summarize how genetic data refute the notion of racial substructure for human populations and address naive interpretations of race across the biological sciences, including those related to ancestry, health, and intelligence, that help to perpetuate racist ideas. A GCC perspective can refute reductionist and determinist claims while providing a more inclusive multidisciplinary framework in which to interpret human variation.

Association of polygenic liabilities for schizophrenia and bipolar disorder with educational attainment and cognitive aging

To elucidate the specific and shared genetic background of schizophrenia (SCZ) and bipolar disorder (BPD), this study explored the association of polygenic liabilities for SCZ and BPD with educational attainment and cognitive aging. Among 106,806 unrelated community participants from the Taiwan Biobank, we calculated the polygenic risk score (PRS) for SCZ (PRSSCZ) and BPD (PRSBPD), shared PRS between SCZ and BPD (PRSSCZ+BPD), and SCZ-specific PRS (PRSSCZvsBPD). Based on the sign-concordance of the susceptibility variants with SCZ/BPD, PRSSCZ was split into PRSSCZ_concordant/PRSSCZ_discordant, and PRSBPD was split into PRSBPD_concordant/PRSBPD_discordant. Ordinal logistic regression models were used to estimate the association with educational attainment. Linear regression models were used to estimate the associations with cognitive aging (n = 27,005), measured by the Mini-Mental State Examination (MMSE), and with MMSE change (n = 6194 with mean follow-up duration of 3.9 y) in individuals aged≥ 60 years. PRSSCZ, PRSBPD, and PRSSCZ+BPD were positively associated with educational attainment, whereas PRSSCZvsBPD was negatively associated with educational attainment. PRSSCZ was negatively associated with MMSE, while PRSBPD was positively associated with MMSE. The concordant and discordant parts of polygenic liabilities have contrasting association, PRSSCZ_concordant and PRSBPD_concordant mainly determined these effects mentioned above. PRSSCZvsBPD predicted decreases in the MMSE scores. Using a large collection of community samples, this study provided evidence for the contrasting effects of polygenic architecture in SCZ and BPD on educational attainment and cognitive aging and suggested that SCZ and BPD were not genetically homogeneous.

Genetic liability estimated from large-scale family data improves genetic prediction, risk score profiling, and gene mapping for major depression

Large biobank samples provide an opportunity to integrate broad phenotyping, familial records, and molecular genetics data to study complex traits and diseases. We introduce Pearson-Aitken Family Genetic Risk Scores (PA-FGRS), a method for estimating disease liability from patterns of diagnoses in extended, age-censored genealogical records. We then apply the method to study a paradigmatic complex disorder, major depressive disorder (MDD), using the iPSYCH2015 case-cohort study of 30,949 MDD cases, 39,655 random population controls, and more than 2 million relatives. We show that combining PA-FGRS liabilities estimated from family records with molecular genotypes of probands improves three lines of inquiry. Incorporating PA-FGRS liabilities improves classification of MDD over and above polygenic scores, identifies robust genetic contributions to clinical heterogeneity in MDD associated with comorbidity, recurrence, and severity and can improve the power of genome-wide association studies. Our method is flexible and easy to use, and our study approaches are generalizable to other datasets and other complex traits and diseases.

Unraveling the shared genetics of common epilepsies and general cognitive ability

PURPOSE

Cognitive impairment is prevalent among individuals with epilepsy, and increasing evidence indicates that genetic factors can underlie this relationship. However, the extent to which epilepsy subtypes differ in their genetic relationship with cognitive function, and information about the specific genetic variants involved remain largely unknown.

METHODS

We investigated the genetic relationship between epilepsies and general cognitive ability (COG) using complementary statistical tools, including linkage disequilibrium score (LDSC) regression, MiXeR and conjunctional false discovery rate (conjFDR). We analyzed genome-wide association study data on COG (n = 269,867) and common epilepsies (n = 27,559 cases, 42,436 controls), including the broad phenotypes 'all epilepsy', focal epilepsies and genetic generalized epilepsies (GGE), as well as specific subtypes. We functionally annotated the identified loci using several biological resources and validated the results in independent samples.

RESULTS

Using MiXeR, COG (11.2k variants) was estimated to be almost four times more polygenic than 'all epilepsy', GGE, juvenile myoclonic epilepsy (JME), and childhood absence epilepsy (CAE) (2.5k - 2.9k variants). The other epilepsy phenotypes were insufficiently powered for MiXeR analysis. We quantified extensive genetic overlap between COG and epilepsy types, but with varying negative genetic correlations (-0.23 to -0.04). COG was estimated to share 2.9k variants with both GGE and 'all epilepsy', and 2.3k variants with both JME and CAE. Using conjFDR, we identified 66 distinct loci shared between COG and epilepsies, including novel associations for GGE (27), 'all epilepsy' (5), JME (5) and CAE (5). The implicated genes were significantly expressed in multiple brain regions. The results were validated in independent samples (COG: p = 3.62 × 10-7; 'all epilepsy': p = 2.58 × 10-3).

CONCLUSION

Our study further dissects the substantial genetic basis shared between epilepsies and COG and identifies novel shared loci. An improved understanding of the genetic relationship between epilepsies and COG may lead to the development of novel comorbidity-targeted epilepsy treatments.

Dissecting the polygenic contribution of attention-deficit/hyperactivity disorder and autism spectrum disorder on school performance by their relationship with educational attainment

Attention-deficit/hyperactivity disorder (ADHD) and autism spectrum disorders (ASD) are strongly associated with educational attainment (EA), but little is known about their genetic relationship with school performance and whether these links are explained, in part, by the genetic liability of EA. Here, we aim to dissect the polygenic contribution of ADHD and ASD to school performance, early manifestation of psychopathology and other psychiatric disorders and related traits by their relationship with EA. To do so, we tested the association of polygenic scores for EA, ADHD and ASD with school performance, assessed whether the contribution of the genetic liability of ADHD and ASD to school performance is influenced by the genetic liability of EA, and evaluated the role of EA in the genetic overlap between ADHD and ASD with early manifestation of psychopathology and other psychiatric disorders and related traits in a sample of 4,278 school-age children. The genetic liability for ADHD and ASD dissected by their relationship with EA show differences in their association with school performance and early manifestation of psychopathology, partly mediated by ADHD and ASD symptoms. Genetic variation with concordant effects in ASD and EA contributes to better school performance, while the genetic variation with discordant effects in ADHD or ASD and EA is associated with poor school performance and higher rates of emotional and behavioral problems. Our results strongly support the usage of the genetic load for EA to dissect the genetic and phenotypic heterogeneity of ADHD and ASD, which could help to fill the gap of knowledge of mechanisms underlying educational outcomes.

Cerebral blood flow regulation and cognitive performance in hypertension

We examined the relation between transcranial Doppler (TCD) markers of cerebral blood flow regulation and cognitive performance in hypertension (HT) patients to evaluate the predictive value of these markers for cognitive decline. We assessed dynamic cerebral autoregulation (dCA), vasoreactivity to carbon dioxide, and neurovascular coupling (NVC) in the middle (MCA) and posterior (PCA) cerebral arteries of 52 patients. Neuropsychological evaluation included the Montreal Cognitive Assessment and tests covering attention, executive function, processing speed, and memory. Notably, reduced rate time in the PCA significantly predicted better processing speed (p = 0.003). Furthermore, reduced overshoot systolic cerebral blood velocity in the PCA and reduced phase in the VLF range in the MCA (p = 0.021 and p = 0.017, respectively) significantly predicted better memory. Intriguingly, enhanced dCA in the MCA predicted poorer memory performance, while reduced NVC in the PCA predicted both superior processing speed and memory performance. These findings suggest that HT-induced changes in cerebral hemodynamics impact cognitive performance. Further research should verify these observations and elucidate whether these changes represent adaptive responses or neurovascular inefficiency. TCD markers might provide insights into HT-related cognitive decline.

Epigenome-wide association study of fluoride exposure during early adolescence and DNA methylation among U.S. children

Exposure to fluoride in early childhood has been associated with altered cognition, intelligence, attention, and neurobehavior. Fluoride-related neurodevelopment effects have been shown to vary by sex and very little is known about the mechanistic processes involved. There is limited research on how fluoride exposure impacts the epigenome, potentially leading to changes in DNA methylation of specific genes regulating key developmental processes. In the Cincinnati Childhood Allergy and Air Pollution Study (CCAAPS), urine samples were analyzed using a microdiffusion method to determine childhood urinary fluoride adjusted for specific gravity (CUFsg) concentrations. Whole blood DNA methylation was assessed using the Infinium MethylationEPIC BeadChip 850 k Array. In a cross-sectional analysis, we interrogated epigenome-wide DNA methylation at 775,141 CpG loci across the methylome in relation to CUFsg concentrations in 272 early adolescents at age 12 years. Among all participants, higher concentrations of CUF were associated with differential methylation of one CpG (p < 6 × 10-8) located in the gene body of GBF1 (cg25435255). Among females, higher concentrations of CUFsg were associated with differential methylation of 7 CpGs; only three CpGs were differentially methylated among males with no overlap of significant CpGs observed among females. Secondary analyses revealed several differentially methylated regions (DMRs) and CpG loci mapping to genes with key roles in psychiatric outcomes, social interaction, and cognition, as well as immunologic and metabolic phenotypes. While fluoride exposure may impact the epigenome during early adolescence, the functional consequences of these changes are unclear warranting further investigation.

Association of psychosocial state with subsequent risk of dementia: a prospective cohort study based on the UK Biobank

BACKGROUND

Multiple psychosocial factors have been associated with dementia, while the individual or joint effects of various psychosocial states on dementia remain unrevealed due to the complex interplay between those factors. Here, the authors examined the associations of psychosocial factors and patterns with subsequent risk of dementia, and if the associations could be modified by genetic susceptibility to dementia.

METHODS

UK Biobank dementia-free participants were followed from one year after recruitment (median date: 24 January, 2010) until 31 October, 2022. Psychosocial states were measured by 22 items related to five dimensions, including psychiatric history, recent stressful life events, current psychiatric symptoms, social contact, and individual socioeconomic state. We identified clusters of individuals with distinct psychosocial patterns using latent class analysis. Cox proportional hazards models were used to evaluate the association between psychosocial items, as well as psychosocial patterns, and risk of dementia. We further performed stratification analyses by apolipoprotein E (APOE) genotype, polygenic risk score (PRS) of dementia, and family history of dementia.

RESULTS

Of 497,787 included participants, 54.54% were female. During a median follow-up of 12.70 years, we identified 9,858 (1.98%) patients with newly diagnosed dementia. We identified seven clusters with distinct psychosocial patterns. Compared to individuals with a pattern of 'good state', individuals with other unfavorable patterns, featured by varying degrees of poor psychological state ('fair state' and 'mildly, moderately, and extremely poor psychological state'), low social contact or socioeconomic state ('living alone' and 'short education years'), were all at an increased risk of dementia (hazard ratios [HR] between 1.29 and 2.63). The observed associations showed no significant differences across individuals with varying APOE genotypes, levels of PRS, and family histories of dementia.

CONCLUSION

Unfavorable psychosocial patterns are associated with an increased risk of dementia, independent of genetic susceptibility. The findings highlight the importance of surveillance and prevention of cognitive decline among individuals with suboptimal psychosocial state.

Bidirectional Two-Sample Mendelian Randomization Analysis Reveals Causal Associations Between Modifiable Risk Factors and Fibromyalgia

Introduction

This study aims to investigate the potential causal effects of modifiable risk factors on Fibromyalgia (FM).

Methods

Genetic variants associated with 34 exposure factors were obtained from Genome-wide association studies (GWAS). Summary statistics for FM were acquired from the FinnGen consortium. Bidirectional Mendelian randomization (MR) analysis was conducted between all exposures and outcomes. The inverse-variance weighted (IVW) method was employed as the primary estimation technique. Heterogeneity and pleiotropy were assessed using MR-PRESSO global test, the weighted median, Cochran's Q statistic and MR-Egger.

Results

Depression (OR=2.087, 95% CI: 1.466-2.971), alcohol consumption (OR=1.489, 95% CI: 1.094-2.028), body fat percentage (OR=1.524, 95% CI: 1.153-2.013) and body mass index (BMI) (OR=1.542, 95% CI: 1.271-1.872) were associated with an increased risk of FM among genetically susceptible individuals. Conversely, higher education level (OR=0.404, 95% CI: 0.297-0.549), longer years of education (OR=0.489, 95% CI: 0.290-0.825) and higher household income (OR=0.328, 95% CI: 0.215-0.502) were protective against FM. Additionally, rheumatoid arthritis (OR=1.138, 95% CI: 1.061-1.221) and ankylosing spondylitis (OR=1.079, 95% CI: 1.021-1.140) were identified as important risk factors for FM.

Conclusion

This MR study unveiled a complex causal relationship between modifiable risk factors and FM. Psychosocial factors significantly increase the odds of FM, while obesity and some autoimmune diseases that frequently coexist with FM demonstrate causal associations. Additionally, lifestyle habits such as alcohol consumption are causally related to FM. Further investigation is needed to determine whether risk factors contribute to the pathogenesis of FM through mechanisms involving central sensitization, inflammatory, and hyperalgesia. This study enhances our understanding of the factors that drive FM onset and progression, offering valuable insights for future targeted prevention and treatment strategies.

Ready, Set, Sort! A User-Guide to Card Sorts for Community-Engaged Empirical Bioethics

We demonstrate the fruitfulness of using card sort activities as an engagement method by detailing community consultation for ethical, legal, and social implications of sociogenomics. Readers are provided with a user-guide for card sort engagement through: (1) an overview of the card sort activity and its merits for engagement, (2) detailed methods of sorting for values-elicitation and prioritization goals, and (3) strategies to design this approach for other participatory research designs. Our intent is to add to meaningful exchanges between community engaged researchers and empirical bioethicists.

Polygenic scores stratify neurodevelopmental copy number variant carrier cognitive outcomes in the UK Biobank

Rare copy-number variants associated with neurodevelopmental conditions (ND-CNVs) exhibit variable expressivity of clinical, physical, behavioural outcomes. Findings from clinically ascertained cohorts suggest this variability may be partly due to additional genetic variation. Here, we assessed the impact of polygenic scores (PGS) and rare variants on ND-CNV carrier fluid intelligence (FI) scores in the UK Biobank. Greater PGS for cognition (PSCog) and educational attainment (PSEA) is associated with increased FI scores in all ND-CNVs (n = 1317), 15q11.2 del. (n = 543), and 16p13.11 dup. carriers (n = 275). No association of rare variants associated with intellectual disability, autism, or putatively loss-of-function, brain-expressed genes was found. Positive predictive values in the first deciles of PScog and PSEA showed a two- to five-fold increase in the rate of low FI scores compared to baseline rates. These findings demonstrate that PGS can stratify ND-CNV carrier cognitive outcomes in a population-based cohort.

The ROSMAP project: aging and neurodegenerative diseases through omic sciences

The Religious Order Study and Memory and Aging Project (ROSMAP) is an initiative that integrates two longitudinal cohort studies, which have been collecting clinicopathological and molecular data since the early 1990s. This extensive dataset includes a wide array of omic data, revealing the complex interactions between molecular levels in neurodegenerative diseases (ND) and aging. Neurodegenerative diseases (ND) are frequently associated with morbidity and cognitive decline in older adults. Omics research, in conjunction with clinical variables, is crucial for advancing our understanding of the diagnosis and treatment of neurodegenerative diseases. This summary reviews the extensive omics research-encompassing genomics, transcriptomics, proteomics, metabolomics, epigenomics, and multiomics-conducted through the ROSMAP study. It highlights the significant advancements in understanding the mechanisms underlying neurodegenerative diseases, with a particular focus on Alzheimer's disease.

Rapid discrimination between deleterious and benign missense mutations in the CAGI 6 experiment

We describe the machine learning tool that we applied in the CAGI 6 experiment to predict whether single residue mutations in proteins are deleterious or benign. This tool was trained using only single sequences, i.e., without multiple sequence alignments or structural information. Instead, we used global characterizations of the protein sequence. Training and testing data for human gene mutations was obtained from ClinVar (ncbi.nlm.nih.gov/pub/ClinVar/), and for non-human gene mutations from Uniprot (www.uniprot.org). Testing was done on post-training data from ClinVar. This testing yielded high AUC and Matthews correlation coefficient (MCC) for well trained examples but low generalizability. For genes with either sparse or unbalanced training data, the prediction accuracy is poor. The resulting prediction server is available online at http://www.mamiris.com/Shoni.cagi6.

Intergenerational transmission of health inequalities: towards a life course approach to socioeconomic inequalities in health - a review

Adult health inequalities are a persistent public health problem. Explanations are usually sought in behaviours and environments in adulthood, despite evidence on the importance of early life conditions for life course outcomes. We review evidence from a broad range of fields to unravel to what extent, and how, socioeconomic health inequalities are intergenerationally transmitted.We find that transmission of socioeconomic and associated health (dis)advantages from parents to offspring, and its underlying structural determinants, contributes substantially to socioeconomic inequalities in adult health. In the first two decades of life-from conception to early adulthood-parental socioeconomic position (SEP) and parental health strongly influence offspring adult SEP and health. Socioeconomic and health (dis)advantages are largely transmitted through the same broad mechanisms. Socioeconomic inequalities in the fetal environment contribute to inequalities in fetal development and birth outcomes, with lifelong socioeconomic and health consequences. Inequalities in the postnatal environment-especially the psychosocial and learning environment, physical exposures and socialisation-result in inequalities in child and adolescent health, development and behavioural habits, with health and socioeconomic consequences tracking into adulthood. Structural factors shape these mechanisms in a socioeconomically patterned and time-specific and place-specific way, leading to distinct birth-cohort patterns in health inequality.Adult health inequalities are for an important part intergenerationally transmitted. Effective health inequality reduction requires addressing intergenerational transmission of (dis)advantage by creating societal circumstances that allow all children to develop to their full potential.

Integrative analysis of causal associations between neurodegenerative diseases and colorectal cancer

Background

Observational studies have shown that the correlation between neurodegenerative diseases and colorectal cancer (CRC) remains controversial. Therefore, this study aimed to verify the causal association between these two diseases.

Methods

Mendelian randomization (MR) analysis was used to assess the causal relationships between five major neurodegenerative diseases and CRC. Multivariable MR (MVMR) analysis was conducted to assess the direct causal effect of neurodegenerative diseases on CRC. Colocalization and pathway enrichment analyses were conducted to further elucidate our results. Sensitivity analysis was conducted to assess the robustness of the results.

Results

Genetically predicted Alzheimer's disease (AD) nominally increased CRC risk (OR = 1.0620, 95%CI = 1.0127-1.1136, P = 0.013). There was no causal effect of genetically predicted CRC on neurodegenerative diseases. Furthermore, we demonstrated that genetically predicted AD marginally increased colon cancer risk (OR = 1.1621, 95%CI = 1.0267-1.3153, P = 0.017). Genetically predicted Lewy body dementia (LBD) had a significant causal effect on the increasing risk of colon cancer (IVW OR = 1.1779, 95%CI = 1.0694-1.2975, P = 0.001). MVMR indicated that effect of AD on colon cancer was driven by LBD, type 2 diabetes, body mass index, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, triglyceride, total cholesterol (TC), processed meat consumption, smoking, alcohol consumption, and educational attainment, whereas the effect of LBD on colon cancer was only influenced by TC. Colocalization and pathway enrichment analysis suggested that LBD and colon cancer possibly shared causal variants (nearby gene APOE), and ERBB4 signaling and lipid metabolism may mediate the causal association between LBD and colon cancer. Sensitivity analysis confirmed the reliability of our findings.

Conclusions

Our study demonstrated that genetic vulnerabilities to AD nominally increased the overall risk of CRC and colon cancer. Genetically predicted LBD indicated an elevated risk of colon cancer, potentially linked to ERBB4 signaling and lipid metabolism.

Protein Identification for Stroke Progression via Mendelian Randomization in Million Veteran Program and UK Biobank

BACKGROUND

Individuals who have experienced a stroke, or transient ischemic attack, face a heightened risk of future cardiovascular events. Identification of genetic and molecular risk factors for subsequent cardiovascular outcomes may identify effective therapeutic targets to improve prognosis after an incident stroke.

METHODS

We performed genome-wide association studies for subsequent major adverse cardiovascular events (MACE; ncases=51 929; ncontrols=39 980) and subsequent arterial ischemic stroke (AIS; ncases=45 120; ncontrols=46 789) after the first incident stroke within the Million Veteran Program and UK Biobank. We then used genetic variants associated with proteins (protein quantitative trait loci) to determine the effect of 1463 plasma protein abundances on subsequent MACE using Mendelian randomization.

RESULTS

Two variants were significantly associated with subsequent cardiovascular events: rs76472767 near gene RNF220 (odds ratio, 0.75 [95% CI, 0.64-0.85]; P=3.69×10-8) with subsequent AIS and rs13294166 near gene LINC01492 (odds ratio, 1.52 [95% CI, 1.37-1.67]; P=3.77×10-8) with subsequent MACE. Using Mendelian randomization, we identified 2 proteins with an effect on subsequent MACE after a stroke: CCL27 ([C-C motif chemokine 27], effect odds ratio, 0.77 [95% CI, 0.66-0.88]; adjusted P=0.05) and TNFRSF14 ([tumor necrosis factor receptor superfamily member 14], effect odds ratio, 1.42 [95% CI, 1.24-1.60]; adjusted P=0.006). These proteins are not associated with incident AIS and are implicated to have a role in inflammation.

CONCLUSIONS

We found evidence that 2 proteins with little effect on incident stroke appear to influence subsequent MACE after incident AIS. These associations suggest that inflammation is a contributing factor to subsequent MACE outcomes after incident AIS and highlights potential novel targets.

Interaction of family SES with children's genetic propensity for cognitive and noncognitive skills: No evidence of the Scarr-Rowe hypothesis for educational outcomes

This study examines the role of genes and environments in predicting educational outcomes. We test the Scarr-Rowe hypothesis, suggesting that enriched environments enable genetic potential to unfold, and the compensatory advantage hypothesis, proposing that low genetic endowments have less impact on education for children from high socioeconomic status (SES) families. We use a pre-registered design with Netherlands Twin Register data (426 ≤ N individuals ≤ 3875). We build polygenic indexes (PGIs) for cognitive and noncognitive skills to predict seven educational outcomes from childhood to adulthood across three designs (between-family, within-family, and trio) accounting for different confounding sources, totalling 42 analyses. Cognitive PGIs, noncognitive PGIs, and parental education positively predict educational outcomes. Providing partial support for the compensatory hypothesis, 39/42 PGI × SES interactions are negative, with 7 reaching statistical significance under Romano-Wolf and 3 under the more conservative Bonferroni multiple testing corrections (p-value < 0.007). In contrast, the Scarr-Rowe hypothesis lacks empirical support, with just 2 non-significant and 1 significant (not surviving Romano-Wolf) positive interactions. Overall, we emphasise the need for future replication studies in larger samples. Our findings demonstrate the value of merging social-stratification and behavioural-genetic theories to better understand the intricate interplay between genetic factors and social contexts.

Replication of Known and Identification of Novel Associations in Biobank-Scale Datasets: A Survey Using UK Biobank and FinnGen

Over the last two decades, numerous genome-wide association studies (GWAS) have been performed to unveil the genetic architecture of human complex traits. Despite multiple efforts aimed at the trans-biobank integration of GWAS results, no systematic analysis of the variant-level properties affecting the replication of known associations (or identifying novel ones) in genome-wide meta-analysis has yet been performed using biobank-scale data. To address this issue, we performed a systematic comparison of GWAS summary statistics for 679 complex traits in the UK Biobank (UKB) and FinnGen (FG) cohorts. We identified 37,148 index variants with genome-wide associations with at least one trait in either cohort or in the meta-analysis, only 3528 (9.5%) of which were shared between UKB and FG. Nearly twice as many variants (6577) were replicated in another dataset at the significance level adjusted for the number of variants selected for replication. However, as many as 9230 loci failed to be replicated. Moreover, as many as 5813 loci were observed as significant associations only in meta-analysis results, highlighting the importance of trans-biobank meta-analysis efforts. We showed that variants that failed to replicate in UKB or FG tend to correspond to rare, less pleiotropic variants with lower effect sizes and lower LD score values. Genome-wide associations specific to meta-analysis were also enriched in low-effect variants; however, such variants tended to be more common and have more consistent frequencies between populations. Taken together, our results show a relatively high rate of non-replication of genome-wide associations in the studied cohorts and highlight both widely appreciated and less acknowledged properties of the associations affecting their identification and replication.

Cognitive performance's critical role in the progression from educational attainment to moderate to vigorous physical activity: insights from a Mendelian randomization study

Introduction

In individuals with high educational levels, moderate to vigorous physical activity (MVPA) is often elevated, yet the causal direction and the role of cognitive performance in this association remain ambiguous. Herein, Mendel randomization (MR) was employed to measure the causal relationship between education, cognitive performance, and moderate to vigorous physical activity. The purpose of this study was to analyze the causal effects of educational attainment on moderate-to-vigorous physical activity (MVPA) levels and to explore potential mediating factors.

Methods

Two-sample univariate MR analysis was conducted to assess the overall effect of education on moderate to severe physical activity. Besides, a two-step MR analysis was carried out to evaluate the mediating effect of cognitive performance on the impact of education on moderate to severe physical activity. Individuals included were exclusively of European ancestry, with data gathered from extensive genome-wide association studies (GWAS) on education (n = 470,941), cognitive performance (n = 257,841), and moderate-to-vigorous physical activity (MVPA) (n = 377,234). Educational attainment was measured by college graduation status. Cognitive performance encompasses not only psycho-motor speed, memory, and abstract reasoning abilities but also knowledge and skills acquired in professional domains. MVPA is defined as any physical activity that produces a metabolic equivalent (MET) of ≥3.0.

Results

The positive two-sample MR analysis showed that education level had a significant protective effect on MVPA deficiency (β = -0.276, 95% CI = -0.354 to -0.199, p = 2.866 × 10-12). However, the reverse two-sample MR analysis showed that MVPA had no significant causal relationship with education level (p = 0.165). Subsequently, the two-step MR analysis indicated that the potential causal protective effect of education on the risk of MVPA deficiency was mostly mediated by cognitive performance (mediating effect β = -0.235, 95% CI = -0.434 to -0.036, and the intermediary ratio was 85.061%).

Discussion

Cognitive performance holds considerable significance in the relationship between education level and MVPA. Consequently, the intervention of cognitive performance may greatly improve the risk of physical inactivity caused by education, thereby promoting individual health.

Biomarkers as proxies for cognitive reserve: The role of high density lipoprotein cholesterol in first episode of psychosis

INTRODUCTION

The proxies used to compose cognitive reserve (CR) for patients of a first episode of psychosis (FEP) have varied in the literature. The development of FEP is linked to peripheral pathways of the central nervous system, yet despite this knowledge, no research has considered the introduction of biomarkers as proxies for CR. Meanwhile, schizophrenia has been linked to the metabolic system, indicating that alterations in the levels of biological parameters, in particular high-density lipoproteins (HDL), cause worse global functioning and cognitive impairment. For these reasons, the present study aimed to create a quantifiable and objective CR index that adjusts for the multifactorial nature of FEP.

MATERIALS AND METHODS

We included 668 FEP patients and 217 healthy controls. Participants were assessed for sociodemographic information, years of education, employment status, premorbid IQ and biological parameters: waist circumference, hypertension, and levels of HDL, triglycerides, and glucose.

RESULTS

The findings suggest that the years of education proxy showed correlational and higher relationship with HDL levels for both FEP patients (r=0.23, b=0.185) and controls (r=0.31, b=0.342). We found that the CR index composed of years of education and HDL levels showed a higher explanatory power for the phenomenon than the classical CR index composed of years of education, employment status and premorbid IQ.

CONCLUSIONS

This article proposes an objective and quantifiable method to measure CR that is more the multifactorial nature of FEP.